GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Echinicola vietnamensis KMM 6221, DSM 17526

Align L-serine dehydratase, alpha chain; SDH; EC 4.3.1.17; L-serine deaminase; L-SD (uncharacterized)
to candidate Echvi_0600 Echvi_0600 L-serine dehydratase, iron-sulfur-dependent, alpha subunit

Query= curated2:P33073
         (292 letters)



>FitnessBrowser__Cola:Echvi_0600
          Length = 302

 Score =  204 bits (519), Expect = 2e-57
 Identities = 114/279 (40%), Positives = 163/279 (58%), Gaps = 3/279 (1%)

Query: 10  DVCNERGIKIYDLVLEEEIKNSHTTEEEIRKKLDAVIDVMHASATKNLTQSDVTEYKMID 69
           + C  + + +Y  V+E E      +EE+I + L +   VM  +    L +  V+   MI+
Sbjct: 13  EYCEAKNVPLYAPVMEYEKDQRGKSEEQIWEGLRSAYKVMKDAVETGLKEEMVSRSGMIN 72

Query: 70  GFAKRTYEYANSGKSIVGDFLAKAMAMAFSTSEVNASMGKIVAAPTAGSSGIMPAMLVAA 129
             AK+ Y +     S++     + ++ A +  EVN+ MG++VAAPTAG+SGI+P  L   
Sbjct: 73  NGAKKVYHHP---LSVLSPEFQRLISRALAAKEVNSCMGRVVAAPTAGASGILPGTLYTL 129

Query: 130 TEKYNFDRTTIQNGFLTSIGIGQVITKYATFAGAEGGCQAECGSASAMAAAALVEMLGGT 189
            E +      +  G L   G+  +I + A+ AGA GGCQAE GSA+AMA+ A+V  LGG 
Sbjct: 130 QEIHGLSDDKVLEGLLIGAGVALIIEQNASLAGAVGGCQAETGSAAAMASGAMVYCLGGN 189

Query: 190 VEQALHAASITIINVLGLVCDPIAGLVQYPCTFRNASGVINAFISADLALAGVESLVPFD 249
            +Q  +A +ITI  +LGLVCDP+AGLV+ PC  RNAS    A  SA +ALA V  ++P D
Sbjct: 190 TDQVFNAVAITIQCMLGLVCDPVAGLVEIPCVVRNASAAAIANSSAQIALADVSGVIPVD 249

Query: 250 EVVIAMGEVGNSMIEALRETGLGGLAGSKTGQKIRRDFL 288
           E V AMGE+G SM    +ET LGGLA + TG+ I +  L
Sbjct: 250 ECVEAMGEIGASMENKYKETALGGLAATLTGKGIAKKVL 288


Lambda     K      H
   0.317    0.132    0.361 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 201
Number of extensions: 6
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 292
Length of database: 302
Length adjustment: 26
Effective length of query: 266
Effective length of database: 276
Effective search space:    73416
Effective search space used:    73416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate Echvi_0600 Echvi_0600 (L-serine dehydratase, iron-sulfur-dependent, alpha subunit)
to HMM TIGR00718 (sdaAA: L-serine dehydratase, iron-sulfur-dependent, alpha subunit (EC 4.3.1.17))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00718.hmm
# target sequence database:        /tmp/gapView.31186.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00718  [M=300]
Accession:   TIGR00718
Description: sda_alpha: L-serine dehydratase, iron-sulfur-dependent, alpha subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                            Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    3.6e-83  265.0   7.3    4.4e-83  264.8   7.3    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0600  Echvi_0600 L-serine dehydratase,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0600  Echvi_0600 L-serine dehydratase, iron-sulfur-dependent, alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.8   7.3   4.4e-83   4.4e-83       6     287 ..       9     288 ..       4     297 .. 0.96

  Alignments for each domain:
  == domain 1  score: 264.8 bits;  conditional E-value: 4.4e-83
                            TIGR00718   6 kelievtkekqikisdlvleeeikvsektkeeirkkldavldvmeaavqknl.esvvsetklidGdakklqeyi 78 
                                          +   e ++ k++ ++  v+e e ++  k++e+i + l +  +vm+ av+ +l e  vs+ ++i+  akk++++ 
  lcl|FitnessBrowser__Cola:Echvi_0600   9 QGWKEYCEAKNVPLYAPVMEYEKDQRGKSEEQIWEGLRSAYKVMKDAVETGLkEEMVSRSGMINNGAKKVYHHP 82 
                                          556688999*******************************************9999**************9876 PP

                            TIGR00718  79 rsGkslvGdllldavakavatsevnaamGkivaaptaGsaGvvpatlvavkeklnfdreqiirflltaiaiGfv 152
                                              s+  + +   +++a+a++evn++mG++vaaptaG++G++p+tl++ +e    + +++ ++ll  +++  +
  lcl|FitnessBrowser__Cola:Echvi_0600  83 L---SVLSPEFQRLISRALAAKEVNSCMGRVVAAPTAGASGILPGTLYTLQEIHGLSDDKVLEGLLIGAGVALI 153
                                          5...5667788999************************************************************ PP

                            TIGR00718 153 vakyasiaGaeGGcqaevGsasamaaaalvemlGGtveqaleaaaitlknvlGlvcdpvaGlvevpcvkrnasG 226
                                          + ++as+aGa GGcqae Gsa+ama+ a+v  lGG ++q  +a+ait++ +lGlvcdpvaGlve+pcv rnas 
  lcl|FitnessBrowser__Cola:Echvi_0600 154 IEQNASLAGAVGGCQAETGSAAAMASGAMVYCLGGNTDQVFNAVAITIQCMLGLVCDPVAGLVEIPCVVRNASA 227
                                          ************************************************************************** PP

                            TIGR00718 227 vinaliaadlalaGveslvpfdevviamykvGqsmiealretGlGGlaasktGrklekdil 287
                                          ++ a  +a++ala v   +p+de v+am+++G sm +  +et lGGlaa+ tG+ + k++l
  lcl|FitnessBrowser__Cola:Echvi_0600 228 AAIANSSAQIALADVSGVIPVDECVEAMGEIGASMENKYKETALGGLAATLTGKGIAKKVL 288
                                          **********************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (300 nodes)
Target sequences:                          1  (302 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.53
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory